Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_004313983.1 C665_RS13205 amino-acid N-acetyltransferase
Query= BRENDA::Q6V1L5 (301 letters) >NCBI__GCF_000310185.1:WP_004313983.1 Length = 438 Score = 139 bits (349), Expect = 2e-37 Identities = 97/278 (34%), Positives = 148/278 (53%), Gaps = 15/278 (5%) Query: 20 ALPYLQQFAGRTVVVKYGGAAMKQEELKEAVMRDIVFLACVGMRPVVVHGGGPEINAWLG 79 A PY+ F GRT VV +GG + +++ D LA +G+R V+VHG P+I+A L Sbjct: 15 AAPYIHAFRGRTFVVGFGGEVAAGKRA-QSLAYDCNLLAALGIRLVLVHGARPQIDAELA 73 Query: 80 RVGIEPQFHNGLRVTDADTMEVVEMVLVGRVNKDIVSRINTTGGRAVGFCG-----TDGR 134 R G+EP+FH+GLRVTDAD +E V+ + V + V + + G G T G Sbjct: 74 RRGLEPRFHHGLRVTDADALECVKSAMA--VTRFEVEALLSQGLPNTPMAGSYIRVTGGN 131 Query: 135 LVLARP---HDQEGIGFVGEVNSVNSEVIEPLLERGYIPVISSVAADENGQSFNINADTV 191 + ARP D + G V + +E I L++ + +I+ + G+ FN+ + V Sbjct: 132 FITARPVGVVDGVDYQYTGAVRKIIAEEINADLDQQNVVLITPLGVSPAGEIFNLAMEEV 191 Query: 192 AGEIAAALNAEKLILLTDTRGIL-EDPKRPESLIPRLNIPQSRELIAQGIVGGGMIPKVD 250 A +A AL AEKLI L D G+L ED + ES+ + Q + +G+ + + Sbjct: 192 AEAVAVALKAEKLIYLCDAPGLLGEDGQLVESV--TADEAQGKLETGEGLT-EDLHLFLP 248 Query: 251 CCIRSLAQGVRAAHIIDGRIPHALLLEIFTDAGIGTMI 288 C IR++ +GV H+ID + LLLE FT AG+GT++ Sbjct: 249 CAIRAVKKGVARCHLIDHDLDGGLLLEFFTHAGVGTVV 286 Lambda K H 0.320 0.139 0.406 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 319 Number of extensions: 19 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 301 Length of database: 438 Length adjustment: 29 Effective length of query: 272 Effective length of database: 409 Effective search space: 111248 Effective search space used: 111248 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory